Time Crisis
by Tarkana262
Summary: Sequel to The Emotional Illness and Life Among the Distant Stars. The Doctor returns to Equestria to find it is the center of a gigantic time paradox. He sets off with the mane 6 to fix the problem, but soon finds the threat is larger than he realized...
1. The Return

Time Crisis

**Chapter 1: The Return**

It was a fine day at the Intergalactic Travelling Carnival – or at least, the artificial facsimile of day. Being located on a space freighter, the inhabitants and visitors didn't have the luxury of a natural light cycle, so instead the ship's lights were programmed to mimic the sun of the current system, as to provide the greatest amount of comfort for its customers.

The carnival was a maze of booths, rides and people of all species. From end to end, the deck was filled with sideshows, eateries and toys from across the universe, all come together in order to create the most fantastic carnival of whatever system it travelled into; the managers even constructed their schedule to coincide with many planets' breaks from school in order to maximize the children's attendance.

Among the thousands of children wandering around on this particular stop, there were three adults; one of which, given the way he acted, looked as if he ought to have been a child anyway.

Amy Williams smirked at the Doctor's gleeful antics. "I swear, you're having more fun than we are."

"Oh, come now," the Doctor laughed, "Everyone loves the carnival! And this is the greatest of all! Don't tell me you aren't having any fun."

"But we're adults," Rory Williams said, "This is a bit more on the kiddish side."

"You're just grumpy because you didn't win that giant teddy bear," Amy scoffed.

"Or maybe because the Doctor forced us on a ride that the guide book described as "It's a Small World" on drugs."

"Well, how was I supposed to know that was a bad thing?" the Doctor said defensively. "I've never been there!"

Amy laughed. "He's been from one end of the universe to the other, and he still hasn't been to Disneyland!"

"I always meant to, but it's just so hard to choose _when_. I mean, do you go to the original opening? One of the anniversaries? The introduction of your favorite princess? (Personally, I've always liked Rapunzel, but still – ) And do you go to Disneyland? Disneyworld? Euro Disney? So many choices, so little time!"

He paused to look at a particularly interesting sideshow and almost didn't continue until Amy tapped his shoulder. "Anyway, it's on my list. It's just it keeps getting interrupted by Daleks and ponies and The End of the Universe as We Know It."

Amy stopped. "Wait, wait…_ponies?_"

* * *

What had started as a normal day had descended into madness.

Twilight Sparkle and her friends ran through the streets of Canterlot, chased by monsters unlike anything she had seen or read about before. They had appeared so suddenly that morning, materializing in a flash of gold. Everypony who wasn't fast enough to run away had been devoured; and once they had finished them, they began to chase down the rest.

The casualties were already numerous: guards, shopkeepers, normal ponies on their normal business, only to be eaten by beasts from Tartarus.

Tears began to form at Twilight's eyes. They hadn't been able to save any of them. Not even Spike. Her dear assistant and friend, now gone forever.

The gates of the castle were already waiting open for them; the guards had quickly realized their fence would do no good against the attackers. They formed around the main doors, ready to help survivors in and keep the monsters out.

They were very brave to do so, but Twilight wondered if they knew what would likely happen to them.

"Come on, girls!" She shouted, running through the doors, "We've got to get to the Princesses!"

* * *

"Let me get this straight," Rory said slowly. "In the universe, there is a planet filled with magical talking ponies."

"Yes," said the Doctor.

"And you've been to this planet."

"Yes."

"And in the process, you somehow…became a pony yourself."

"Yes."

"But now you're not."

"Yes," the Doctor repeated. "Is this all really so hard to believe?"

Amy sighed. "I suppose with all we've seen, it shouldn't be."

"It's a lovely place, Equestria," the Doctor said wistfully. "Green pastures, purple mountains, all sorts of supposedly mythical creatures – I really ought to take you there someday." He clapped his hands. "Oh, the girls would love to meet you! Especially Twilight, she was always so curious about everything. I think Rarity would like you, Amy – always so fashion-conscious. Rory, however – that's a hard one. Spike, perhaps? I never did see much of him…"

"Do you have any idea what he's saying?" Rory asked as the Doctor prattled on.

"No," Amy admitted, "But that's really not too different from normal, is it?"

* * *

"Your Highness, more reports of these creatures are coming in from Cloudsdale and Manehatten."

"Send another Pegasus squadron there. Instruct them that they are to only assist in evacuation, not to engage the enemy."

"What of our own defenses, ma'am?"

"Our spears and trebuchets appear to have no effect on them, my lady. I would advise combat magic, but I wouldn't get my hopes up."

"Agreed. Send a detachment of my personal Unicorn guard to join the others at the gates; tell them if their magic proves useless, they are to fall back immediately. I am not sending any of them to their deaths just to delay the inevitable."

The throne room was in chaos. In addition to the Royal Pony Sisters and the Element Bearers, the Equestrian Council and the heads of each division of the military were crowded around tables, at windows, or simply sitting on the floor, trying not to panic. Together, they tried to piece together a workable defense – but they knew they were fighting a losing battle.

A guard ran to Celestia's side. "Your Majesties, the enemy has broken through the main gates."

Luna's head shot up from her own conversation. "But I thought you said they were unable to get through before?"

The guard wore a grave expression. "Yes, my lady, I did."

Celestia sighed. "Then I suppose we have no choice. Begin the final evacuations."

Everyone immediately began to move. The Princesses used their magic to activate a hidden mechanism that opened a hidden passageway, which everyone began to file into.

"Elements of Harmony, wait," Celestia commanded. As they turned to her, she brought out an ornate chest. She opened it and distributed the Jewelry of Harmony between them.

"About time we joined the fight!" Rainbow said.

Celestia shook her head. "No. You are to take the Elements and leave with the others. We have no idea if their power will work on these monsters; if we were to lose you, there would be no hope for the rest of Equestria."

"Then what are we supposed to do?" Applejack asked.

"There is an old spell in Starswirl's Archive," Luna explained, "Penned in the first years of Equestria. It was made to summon a great warrior to aid us in when the kingdom is at its most dire. We have activated it, but we do not know how long it will take, if at all."

"Until then, you must escape from here…" Celestia closed her eyes. "While we make our last stand."

"What?" Twilight cried. "You can't possibly be saying – "

The doors crashed open. The insectoid beasts flew in, setting their sights on Luna and Celestia.

"Goodbye, my faithful student," Celestia said softly. "Remember what I have taught you, and the Sun and Moon will always light your path."

The Princesses turned to face the incoming threat. In unison, they unleashed blasts of pure magic at the monsters. The blows caused them to stagger, but their advance was only slowed.

Luna was the first to fall. The beasts flanked her and caught her by surprise. Celestia gasped, and in that moment of distraction, she, too, was consumed.

Twilight screamed the name of her mentor, and the monsters turned to face them.

* * *

The vision hit the Doctor like a migraine, but it wasn't painful; at least, not physically. It was as if the sender had poured out every ounce of desperation they had in their body so the message could be heard.

He saw a familiar castle on a mountain, but the streets were bare. He saw ponies being hunted and devoured by monsters. He saw two regal alicorns looking at him, pleading to him:

_Save us, Doctor. Equestria needs you._

Amy caught him as he stumbled. "What is it? What's wrong, Doctor?"

The Doctor said nothing as he broke into a run. Amy and Rory followed, and they soon found themselves back at the TARDIS. The Doctor ran around the console in a panic. "No, no, this is bad, very, very bad…"

"What's bad, Doctor? What!" Amy demanded.

"Everything! Not here, but there!" he pointed to the monitor, which showed an Earth-like planet. "Equestria – the planet I was telling you about with the ponies and pegasi and unicorns – something's gone horribly, _horribly_ wrong."

"Well, let's go already," Rory suggested. "You said you wanted to take us there, anyway."

"No!" the Doctor grabbed their shoulders and herded them outside. "You two just got married and are on a nice, quiet honeymoon that will not be interrupted by anything if I can help it, and that certainly includes dragging you into the center of another End of the Universe as We Know It situation! Now, just wait here, I will be back in a moment."

With that, he leaped back into the TARDIS and disappeared.

Amy sighed as the distinctive rumble faded away. "He left us behind. Again."

"Don't worry about it," Rory said, shrugging. "At least we now have some time to ourselves. Besides, he said he'd be back soon."

Amy sat on a nearby bench and frowned. "Last time he said that, I waited for two years."

* * *

Twilight stared at the creatures through tear-clouded eyes. The Princesses were no more. The six of them had lingered too long; taking the secret passage now would doom the others. There was nothing they could do but accept their fate.

"H-hey, girls?" rainbow said hesitantly, "I just wanted to say – "

"We know, Rainbow," Applejack said quietly. "We know. And we feel the same way."

The mares nodded. Silently, they joined hooves and looked each other in the eyes, passing their silent message: if they were to die, they would die together.

They turned to face their attackers. The creatures shrieked as they flew towards them. Twilight closed her eyes, wishing they would just end it –

_VWORP…VWOPR…VWORP…_

The air stirred violently. The monsters stopped, darting across the room in confusion and panic. The mares looked up to see a tall blue box slowly appear in the room.

The door squeaked open, and out walked a gray earth pony colt wearing a tweed jacket and bow tie.

"Hello, hello, hello!" said the Doctor. "Did anyone miss me?"


	2. Truth and Consequences

He had finally come. At the last moment, when all seemed lost, the Doctor flew in at last to save the day.

Twilight didn't know whether to smile or cry.

"Now then!" the Doctor said, looking around the room. "What seems to be the probleOOOHHHH MY GOODNESS!"

The colt had found the monsters, who were floating behind the TARDIS almost bewilderedly.

"Well, you were right to call me! Reapers! In Equestria! Now, what are you doing here? It's alright, the TARDIS' translator is on, go ahead."

_We have crossed before,_ the Reapers responded telepathically. _The Oncoming Storm. The Scourge of the Daleks. You were…taller before._

"Long story. But anyway, what are _you_ doing _here?_ You lot feed on paradoxes, so that means something terrible must have happened."

_The stream has been altered. The flow is dissected, spliced, wrong. Few have noticed, but that will soon change. If we act, it will be confined to this planet._

"At the expense of thousands of lives," the Doctor concluded. "Innocent ponies who had no hand or idea of what's going on. Sorry, that's not going to happen."

_And what else would we do?_ The Reapers asked. _What would the last of the Time Lords, who sacrificed his entire race to stop the Daleks, have us do?_

The Doctor frowned at their mention of his past. "Let me handle it. I can fix this. No one else needs to die."

_So you have a history of saying,_ the Reapers replied, _and yet death is your constant companion. Everywhere you go, bodies are left in your wake._

"I can save them!" the colt shouted. "I don't need you to believe me!"

The Reapers communicated among themselves. _Very well. The center of the paradox can be found in the forest called Everfree. You shall have 48 local hours to mend what has been broken. But if you have not succeeded by that time, you will be consumed with the rest._

And with that, the room flashed and the Reapers disappeared.

"Well, that went well! The colt said, smiling. "Now then, we've got a lot to do and not a lot of time to do it, but certainly more than I was expecting, so that's a good thing – "

_Smack! _"**Where were you?!**"

Twilight glared at the Doctor as he held his cheek where she slapped him. "All of Tartarus is breaking loose, and only now you decide to show up?" _Smack!_ "Everypony is terrified because of you!" _Smack!_ "Canterlot is in chaos because of you!" _Smack!_ "Celestia is dead, **because!**" _Smack!_ "**Of!**" _Smack!_ "**YOU!**" _Smack!_

The unicorn mare fell to the floor as tears streamed from her eyes. Her hits slowly descended to weak thumps against the Doctor's chest. She sobbed as the Doctor slowly drew her into a hug and stroked her mane.

"I'm sorry," he said quietly as she cried. "I'm sorry, I'm sorry, I'm sorry…"

* * *

The sight of the TARDIS' new interior was met with silence. Rarity and Fluttershy escorted a grieving Twilight to the bedrooms in an attempt to comfort her. The rest of the group remained in the main room, silently watching the Doctor pace and occasionally glance up the stairs.

Rarity and Fluttershy returned shortly. Applejack walked to them and talked in a hushed tone. "How is she?"

"She's resting now," Rarity answered with a sigh. "I believe she'll be physically ready to go soon, but…"

"She was…whispering to herself," Fluttershy said.

"The poor dear sounded so confused. Like a schoolfilly trying to work out a homework problem. We tried to talk to her, but all she would talk about was Celestia and time paradoxes."

Applejack shook her head. "Poor girl. Her logical way of thinkin' just isn't made for all this time travel business."

Twilight returned much later, but was still unwilling to speak. The ponies gathered around the Doctor, looking to him for direction.. He didn't look up for a long moment as he pulled his thoughts together. "I'm sorry for what has happened. This is horrible for all of you, but we have to press on.

"Before anyone asks, no, we can't just go back and keep the Reapers from coming. I'm already here, and I can't change my own timeline. The last thing we want is a paradox on top of a paradox.

"I know this doesn't look good, but remember, if we find the source of the paradox and deal with it, everyone will be restored to life. It will be as if this never happened.

"The Reapers said the paradox originated somewhere in the Everfree Forest. The distortion of time is too great in there, so we'll have to land the TARDIS halfway in and walk the rest of the way. From what I've heard, the forest is already a dangerous place, but with the paradox running amuck all sorts of nasty things can and will happen, so I need you to stick together and trust me no matter what. Alright?"

The mares somberly spoke their agreement.

"Right-o," the colt said mirthlessly, "Let's get to it."


	3. A Walk in the Dark

**Author's Note: And we're back, ladies and gentlemen!**

**Sorry for the long absence. I was going through some doubts about my writing and still trying to figure out some troublesome plot details. Nevertheless, it's been worked out now and I hope the story is better for it.**

**Also, I've made another change to the end of Chapter 2. This one's a bit more noticeable, so you may want to reread it if some things in this chapter confuse you.**

* * *

The Everfree Forest was never known for its luminosity, but today it seemed darker than it had ever been. Even the animals knew something was wrong; the forest was silent as the grave, save for the seven ponies cautiously making their way through it.

The Doctor would have liked to have landed the TARDIS closer to their destination, but remembering what had happened during his last encounter with Reapers, landing far from the epicenter was the safest route for now. And so the six walked, consumed by a very uncomfortable silence.

Applejack cleared her throat awkwardly. "So, uh…new look?"

"Hm?" the Doctor said distractedly. "Oh, yes. I regenerated, like I said I was before I left last time. You know, die and get a new body and all that."

"And a new fashion sense, it would seem," said Rarity. "I thought I threw out all your bow ties."

"Oi! Bow ties are cool."

The mare chuckled. "If bow ties are cool, then I'm Princess Celestia."

Rarity's hoof shot to her mouth when she realized what she had said. She glanced at Twilight; the purple unicorn stared dejectedly at the ground.

"So!" Rainbow said loudly when the silence became unbearable. "What do you think's up ahead, Doc? More Reapers? Aliens? An evil wizard?"

"Haven't the slightest idea," the Doctor replied. "But that just adds to the fun!"

"I don't see what's so 'fun' about runnin' in blind," said Applejack.

"It's like reading a mystery novel. The further you go into the story the more clues you get to the villain's identity: their past, what they look like, what they're capable of. If you're paying enough attention, you can figure out whodunit before the author even reveals it! Oooh, that reminds me – Rarity, did I ever tell you about Agatha Christie? Mystery writer, I met her once – brilliant woman! Fooled me every time – well, really only once, but I can tell you – "

A shrill howl filled the forest. The seven ponies stopped in their tracks and huddled together in fear. Slowly, a group of shadows approached them, each with a pair of menacing green eyes.

"Timberwolves!" Applejack shouted.

As if on cue, the wolves leaped at them, forcing them to separate.

"Amazing!" the Doctor laughed, dodging a large set of teeth. "Animals made from nothing but sticks and branches – held together by the psychic energy from their own consciousness's, no doubt. But if that's true, I wonder how they – "

His theorizing was interrupted by Rainbow Dash slamming into him, pushing him out of the reach of a pouncing wolf. "Less science, more fighting!"

The skirmish was soon split into four groups of fighters. Rarity stood close to Fluttershy, protecting the timid Pegasus with her magic. Applejack and Rainbow Dash tag-teamed every timberwolf that came their way, combining their respective strength and speed to keep them at bay. Pinkie Pie, oddly enough, was holding fine on her own; any wolf that hadn't been too confused by her antics was introduced to the business end of her Party Cannon.

The Doctor found himself back-to-back with Twilight Sparkle, using his sonic screwdriver in tandem with her magic.

"Didn't take you for the fighting type, Doctor," Twilight said, speaking for the first time since they left Canterlot.

"I try not to be," he replied, sending a sonic wave that jumbled a wolf's wooden pieces around. "Most of the time, I just stick to running. But then again, I don't usually travel with unicorns."

"I guess you're just lucky to have me around, then."

The ponies fought hard, but it was clear that the timberwolves had no intention of giving up. For every one they knocked down, two more emerged from the shadows. In a matter of minutes, the ponies were surrounded.

"Any particularly brilliant plans?" Rarity asked.

The Doctor clutched his screwdriver. "Listen; I'm going to put the screwdriver on a frequency that should disorient them, but it needs to be close to work. While I'm holding them off, you need to run like you've never before."

"But we can't just leave you!" Rainbow cried.

"This is our only chance, Rainbow Dash. Don't worry about me, I'll catch up with you later."

The stallion leapt forward, holding the screwdriver in his teeth as it emitted a high-pitched whine. "Go! Now!" he grunted through his teeth.

There was no time to argue with the Time Lord. Together, the six mares rushed the timberwolves, who barely noticed them crash through their lines amidst their pain.

The Doctor watched them go for as long as he could see them, and turned back just in time to see a paw swipe at his face, knocking him into a tree.

As consciousness left him, he could almost hear an odd, far away laughter mocking him in his head.

* * *

The Doctor had no way of knowing how long he had been out; the trees let such little light in it was a wonder he could see at all.

As he walked on, he also realized that he had no sense of direction. He had never been to the Everfree Forest before, and the readings from his sonic were so confused with the natural energy from the forest that he could end up wandering in the forest for hours before he even found a way out.

With that came the realization that the six mares were likely no better off than he. Even after their travels together, they didn't know how to handle a paradox like this. Even if they escaped the wolves, they were probably walking into even greater danger.

And finally came the greatest and worst realization of all: that here, in this dark, foreign forest, he was well and truly alone.


	4. Revelation

The Everfree Castle ruins were very different from their Canterlot counterpart. As opposed to gilded halls of white marble, this castle had greyed with age, stripped of everything of value either by the treasury or scavenging ponies. Its design bore a significant resemblance to the human gothic style, further adding to the disconcerting atmosphere surrounding it.

It would have been fascinating to the Doctor under any other circumstance.

He was an odd sight in those halls, especially if one had known him before that moment. Gone was the spring in his step, the air of childish wonder and curiosity; and in its place, a slow trot and the hardened face of a colt that had seen too many wars, and lost too many friends.

He came to a stairway that led up the tallest tower; the same one, he had been told, where Twilight and her friends had defeated Nightmare Moon. His sensitivity to the forces of time told him he would find the source of the paradox there.

The steps almost seemed as if they went on for centuries, but he eventually reached the top, emerging in a room illuminated only by the moon shining faintly through the windows. As he stepped forward, a single shaft of light burst from the ceiling, illuminating a strange creature – one the Doctor had seen before.

"Hello, Doctor," it said with a bow. "It's so good to see you again."

The Doctor scowled. "_Discord._ I thought you had been driven from the universe."

"Oh, that was simply some of my puppets. I simply had the great displeasure of being turned to stone for a millennia."

"So this is where you were," said the Doctor. "Right under everyone's noses. That explains why the Pantheon lost so much ground."

Discord chuckled. "Ah, yes. The so-called 'Pantheon of Discord.' That was never my idea, you know. Some beings simply decided that I was some sort of god, and I felt no need to tell them otherwise." His sighed wistfully. "Can you imagine it, Doctor? A whole bunch of transcendental beings, dedicated to the cause of chaos, spread out across the universe! Truly a beautiful sight."

"So where does Equestria fit in all of this?" The colt asked. "Why this of all planets?"

The Draconequus laughed again. "Believe it or not, my dear time pony, I am actually a native to this world. I even ruled it for a while in the good old days; the Equestrian government was so weak in its early days, it had no defense against my chaos."

"But then Celestia and Luna defeated you," the Doctor pointed out. "They turned you into stone for a thousand years, as you said."

Discord pulled an abacus out of nowhere and began to count. "One thousand, three hundred seventy-two years, twenty-five days, five hours, twelve minutes and forty-eight seconds, to be exact. And then I broke free, had some fun with Ponyville, demoralized the Elements of Harmony, and quite nearly won again, before that bookworm broke my spells."

The Doctor smirked. "Good old Twilight Sparkle."

"And here we are; the last Time Lord – or Time Pony, I suppose is more accurate right now - and the Spirit of Chaos. I suppose you want to hear how this all happened before we start anything else?"

Discord leaned back as if he was sitting in an invisible hammock. "I do think you'll like this one, Doctor, as you are directly involved in it."

The Doctor's face fell.

"You might be wondering why I didn't simply leave the planet as soon as I escaped, maybe try to conquer some other, less magically-inclined world instead. The truth is, someone, somewhere decided it would be funny if they gave my power a very specific limit: I cannot use it to leave this planet.

"But one day while I sat in my stone prison, something happened: you showed up. The last Time Lord…and my escape.

"You know of the Time Rift that runs underneath Canterlot; you used it to recharge your time machine before you left that last time. But what you never realized is that whenever you used your machine, the rift released a burst of energy. It was for the most part unnoticeable – a few flowers wilted a little early – but it did wonders for my cage."

The Doctor's eyesd widened. "You mean…every time I used the TARDIS took time off your sentence?"

"And now I am free!" Discord laughed. "But I was not done with you yet, Doctor. So I reached into the rift and shuffled things around a bit. The Reapers weren't too terribly happy about that, but I got what I wanted: you came running, and I was able to snatch this." He snapped his fingers, and in a puff of smoke revealed –

"My TARDIS!" the Doctor yelled.

"She's a tough little girl; I still haven't been able to crack her open," Discord lamented. "But it won't be too long before I can use her to do what my power can't. And then I will reclaim my Pantheon, and nothing in the galaxy will stand in my way!"

"You will do no such thing!" The colt stomped the floor. "Because you've forgotten one thing. Well, six things, plus me."

Discord grinned slowly. "Oh, my dear Time Pony, I'm fairly sure I did remember those."

He swung his arm behind him, and from the shadows, the six mares stepped out - but something was wrong with them. They all wore scowls on their faces, and their coats were desaturated, turned to a dull gray.

"Allow me to introduce my Elements of Chaos;" Discord said, walking behind the ponies in a line. "Treachery. Wrath. Greed. Deception. Cruelty." He stopped at Twilight and stroked her mane. "And Chaos makes it all complete."

The Doctor couldn't move. Everything had gone horribly wrong.

"And you know what the best part of all this is?" Discord taunted. "It's that I have you to thank for everything, Doctor. You set me free, you gave me a way off the planet, and you gave me my first minions. If it wasn't for you, _none of this would have happened._"

"No…No! I can still stop you!"

Discord laughed loudly. "You and what army, Time Pony? Celestia is Reaper food, your friends are mine! And now it is time for you to go."

He snapped his fingers, causing a portal to appear behind the Doctor and slowly approach him. The colt began to yell: "This isn't over, Discord! As long as I live, I will not stop until Equestria is safe! I will be - "

But whatever he said next was lost as the portal enveloped him and the room fell to silence.

"Come now my little ponies!" Discord called to his companions. "We have a machine to crack, glorious chaos to make, and all the time in the universe to do it."


	5. To the Fans of Time Crisis

**It is with great sorrow that I must announce that Time Crisis will be discontinued.**

**The fact of the matter is that I just don't have any inspiration or drive to continue the story, and I feel like I need to put it behind me if I'm going to move on in my writing. I'm sorry, I know what I said before, and I really don't want to give up on this story, but I have to.**

**Thank you to everyone who read, fav'd and commented on the trilogy, such as it is. I had a lot of fun writing it, but it's time for me to move on.**


End file.
